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- PDB-8oz0: Structure of a human 48S translation initiation complex with eIF4... -
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Basic information
Entry | Database: PDB / ID: 8oz0 | ||||||||||||
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Title | Structure of a human 48S translation initiation complex with eIF4F and eIF4A | ||||||||||||
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![]() | TRANSLATION / eIF4A / eIF4F / initiation / ribosome / mRNA | ||||||||||||
Function / homology | ![]() positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / eukaryotic initiation factor eIF2 binding / male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / eukaryotic initiation factor eIF2 binding / male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation / Cellular response to mitochondrial stress / positive regulation of translation in response to endoplasmic reticulum stress / response to manganese-induced endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Recycling of eIF2:GDP / translation reinitiation / PERK-mediated unfolded protein response / regulation of cellular response to stress / eukaryotic initiation factor 4E binding / IRES-dependent viral translational initiation / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / regulation of translational initiation in response to stress / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / multi-eIF complex / eukaryotic translation initiation factor 3 complex / selenocysteine metabolic process / RNA cap binding / eukaryotic translation initiation factor 4F complex / selenocysteine incorporation / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / cytoplasmic translational initiation / Deadenylation of mRNA / translation factor activity, RNA binding / mRNA cap binding / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / miRNA-mediated gene silencing by inhibition of translation / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / eukaryotic 48S preinitiation complex / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / M-decay: degradation of maternal mRNAs by maternally stored factors / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / IRE1-RACK1-PP2A complex / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / metal-dependent deubiquitinase activity / positive regulation of protein localization to cell periphery / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / GDP-dissociation inhibitor activity / ubiquitin-like protein conjugating enzyme binding / regulation of translational initiation / regulation of establishment of cell polarity / negative regulation of phagocytosis / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / protein kinase A binding / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / pigmentation / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Brito Querido, J. / Sokabe, M. / Diaz-Lopez, I. / Gordiyenko, Y. / Fraser, C.S. / Ramakrishnan, V. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Authors: Jailson Brito Querido / Masaaki Sokabe / Irene Díaz-López / Yuliya Gordiyenko / Christopher S Fraser / V Ramakrishnan / ![]() ![]() Abstract: Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), ...Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), which then scans along the mRNA until the start codon is recognized. We have previously shown that eIF4F binds near the mRNA exit channel of the 43S, leaving open the question of how mRNA secondary structure is removed as it enters the mRNA channel on the other side of the 40S subunit. Here we report the structure of a human 48S that shows that, in addition to the eIF4A that is part of eIF4F, there is a second eIF4A helicase bound at the mRNA entry site, which could unwind RNA secondary structures as they enter the 48S. The structure also reveals conserved interactions between eIF4F and the 43S, probaby explaining how eIF4F can promote mRNA recruitment in all eukaryotes. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 2.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 287.4 KB | Display | |
Data in CIF | ![]() | 494.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 17297MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Eukaryotic translation initiation factor ... , 18 types, 18 molecules 5678ABCDEFGHIJKUx2
#1: Protein | Mass: 52281.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Eukaryotic translation initiation factor 3 subunit E Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 37593.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit F Source: (natural) ![]() |
#3: Protein | Mass: 35662.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit G Source: (natural) ![]() |
#4: Protein | Mass: 39979.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit H Source: (natural) ![]() |
#6: Protein | Mass: 166903.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit A Source: (natural) ![]() |
#7: Protein | Mass: 25083.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit K Source: (natural) ![]() |
#8: Protein | Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit M Source: (natural) ![]() |
#9: Protein | Mass: 36161.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 2 subunit 1 Source: (natural) ![]() |
#10: Protein | Mass: 51178.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 2 subunit 3 Source: (natural) ![]() |
#11: Protein | Mass: 36543.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit I Source: (natural) ![]() |
#12: Protein | Mass: 16488.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Eukaryotic translation initiation factor 1A / Source: (gene. exp.) ![]() ![]() ![]() |
#13: Protein | Mass: 49301.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Eukaryotic translation initiation factor 5 / Source: (gene. exp.) ![]() ![]() ![]() |
#14: Protein | Mass: 92593.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit B Source: (natural) ![]() |
#15: Protein | Mass: 105503.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit C Source: (natural) ![]() |
#16: Protein | Mass: 66803.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit L Source: (natural) ![]() |
#26: Protein | Mass: 38454.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 2 subunit 2 Source: (natural) ![]() |
#52: Protein | Mass: 64060.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Eukaryotic translation initiation factor 3 subunit D Source: (natural) ![]() |
#56: Protein | Mass: 155130.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Eukaryotic translation initiation factor 4 gamma / Source: (gene. exp.) ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules 9
#5: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 60S ribosomal protein L41 / Source: (natural) ![]() |
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+40S ribosomal protein ... , 30 types, 30 molecules LMNOPQRSTVXYZabcdefghijlmoqsvw
-RNA chain , 3 types, 3 molecules Wyz
#28: RNA chain | Mass: 555083.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 18S rRNA / Source: (natural) ![]() |
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#53: RNA chain | Mass: 24231.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Human initiator Met-tRNA-i / Source: (synth.) ![]() |
#54: RNA chain | Mass: 67626.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: mRNA / Source: (synth.) ![]() |
-Protein , 4 types, 5 molecules knp31
#42: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Receptor of activated protein C kinase 1 / Source: (natural) ![]() |
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#45: Protein | Mass: 17630.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein uS13 / Source: (natural) ![]() |
#47: Protein | Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Small ribosomal subunit protein eS31 / Source: (natural) ![]() |
#55: Protein | Mass: 46207.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Eukaryotic initiation factor 4A-I / Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 2 types, 91 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#57: Chemical | #58: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human 48S translation initiation complex / Type: COMPLEX / Entity ID: #1-#56 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 47.88 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 241389 / Symmetry type: POINT | ||||||||||||||||||||||||
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